SIGNOR 3.0 parser. Updated to map SIGNOR phenotypes to GO terms when …

[beasleyjonm]

Updated to map SIGNOR phenotypes to GO terms when available from their mappings. A similar mapping process can be repeated for the complexes, protein families, and stimuli terms if SIGNOR ever updates their mappings.

[matentzn]

Sorry just lurking but noticed the constants might be reversed (signor values in sgd and the other way around)

[beasleyjonm]

Oh my bad!! Thanks for catching this.

[matentzn]

Sorry I don't know enough about your project to review, I am a colleague of @DnlRKorn from an entirely different KG land.. 😂 good luck with your work!

[eKathleenCarter]

@beasleyjonm

Currently, it cannot be run as written.

1. SIGNOR-ST.csv, SIGNOR-PH.csv files are not included.
2. self.data_path not set.

Please add files and define variable

[EvanDietzMorris]

self.data_path is actually set in the init of the SourceDataLoader interface, which all parsers inherit from, and should call with super().init so that is not an issue. Maybe not the easiest to read code design but that's how it works for all them.

ORION/Common/loader_interface.py

Lines 32 to 37 in b124dfb

	if source_data_dir:
	self.data_path = os.path.join(source_data_dir, "source")
	if not os.path.exists(self.data_path):
	os.mkdir(self.data_path)
	else:
	self.data_path = os.environ.get("ORION_STORAGE")